Human Immunodeficiency Virus Type 1 (HIV-1) Subtype B Epidemic in Panama Is Mainly Driven by Dissemination of Country-Specific Clades

The Human immunodeficiency virus type-1 (HIV-1) subtype B is the most predominant clade in Central America; but information about the evolutionary history of this virus in this geographic region is scarce. In this study, we reconstructed the spatiotemporal and population dynamics of the HIV-1 subtype B epidemic in Panama. A total of 761 HIV-1 subtype B pol sequences obtained in Panama between 2004 and 2013 were combined with subtype B pol sequences from the Americas and Europe. Maximum Likelihood phylogenetic analyses revealed that HIV-1 subtype B infections in Panama derived from the dissemination of multiple founder viruses. Most Panamanian subtype B viruses (94.5%) belong to the pandemic viral strain proposed as originated in the US, whereas others (5.5%) were intermixed among non-pandemic Caribbean strains. The bulk (76.6%) of subtype B sequences from Panama grouped within 12 country-specific clades that were not detected in other Central American countries. Bayesian coalescent-based analyses suggest that most Panamanian clades probably originated between the early 1970s and the early 1980s. The root location of major Panamanian clades was traced to the most densely populated districts of Panama province. Major Panamanian clades appear to have experienced one or two periods of exponential growth of variable duration between the 1970s and the 2000s, with median growth rates from 0.2 to 0.4 year^{− 1}. Thus, the HIV-1 subtype B epidemic in Panama is driven by the expansion of local viral strains that were introduced from the Caribbean and other American countries at an early stage of the AIDS pandemic.     

1992—1994年HIV—1国际流行株和云南株膜蛋白V3区氨基酸共有序列比较

对１９９２～１９９４年间１６个云南ＨＩＶ１株膜蛋白基因Ｖ３区进行了ＤＮＡ序列测定,经计算机ＤＮＡＳＩＳ及ＰＲＯＳＩＳ软件进行同源性分析,得出其相应的氨基酸共有序列ＹＮＶ３和两组共有序列ＹＮＶ３Ａ和ＹＮＶ３Ｂ,计算了ＹＮＶ３中每个氨基酸的保守性。分别将ＹＮＶ３Ａ和ＹＮＶ３Ｂ与世界各地的ＨＩＶ１代表株的相应序列进行了同源性比较。结果表明,ＨＩＶ１云南株膜蛋白Ｖ３区氨基酸共有序列ＹＮＶ３中每个氨基酸的平均变异度为７．６６％。两组共有序列ＹＮＶ３Ａ和ＹＮＶ３Ｂ,分别与ＨＩＶ１美欧株及泰国流行株Ｂ亚群相应序列有较高同源性。这一结果提示,在进化上云南瑞丽ＨＩＶ１流行毒株间有非常密切的关系,在这一时期该地区的流行毒株以ＨＩＶ１美欧株、泰国株Ｂ亚群及其衍生株为主。     

Spatiotemporal Dynamics of Dissemination of Non-Pandemic HIV-1 Subtype B Clades in the Caribbean Region

The Human immunodeficiency virus type-1 (HIV-1) epidemic in the Caribbean region is mostly driven by subtype B; but information about the pattern of viral spread in this geographic region is scarce and different studies point to quite divergent models of viral dissemination. In this study, we reconstructed the spatiotemporal and population dynamics of the HIV-1 subtype B epidemic in the Caribbean. A total of 1,806 HIV-1 subtype B pol sequences collected from 17 different Caribbean islands between 1996 and 2011 were analyzed together with sequences from the United States (n = 525) and France (n = 340) included as control. Maximum Likelihood phylogenetic analyses revealed that HIV-1 subtype B infections in the Caribbean are driven by dissemination of the pandemic clade (B_PANDEMIC) responsible for most subtype B infections across the world, and older non-pandemic lineages (B_CAR) characteristics of the Caribbean region. The non-pandemic B_CAR strains account for >40% of HIV-1 infections in most Caribbean islands; with exception of Cuba and Puerto Rico. Bayesian phylogeographic analyses indicate that B_CAR strains probably arose in the island of Hispaniola (Haiti/Dominican Republic) around the middle 1960s and were later disseminated to Trinidad and Tobago and to Jamaica between the late 1960s and the early 1970s. In the following years, the B_CAR strains were also disseminated from Hispaniola and Trinidad and Tobago to other Lesser Antilles islands at multiple times. The B_CAR clades circulating in Hispaniola, Jamaica and Trinidad and Tobago appear to have experienced an initial phase of exponential growth, with mean estimated growth rates of 0.35–0.45 year⁻¹, followed by a more recent stabilization since the middle 1990s. These results demonstrate that non-pandemic subtype B lineages have been widely disseminated through the Caribbean since the late 1960s and account for an important fraction of current HIV-1 infections in the region.     

Origin and dynamics of HIV-1 subtype C infection in India

Objective

To investigate the geographical origin and evolution dynamics of HIV-1 subtype C infection in India.

Design

Ninety HIV-1 subtype C env gp120 subtype C sequences from India were compared with 312 env gp120 reference subtype C sequences from 27 different countries obtained from Los Alamos HIV database. All the HIV-1 subtype C env gp120 sequences from India were used for the geographical origin analysis and 61 subtype C env gp120 sequences with known sampling year (from 1991 to 2008) were employed to determine the origin of HIV infection in India.

Methods

Phylogenetic analysis of HIV-1 env sequences was used to investigate the geographical origin and tMRCA of Indian HIV-1 subtype C. Evolutionary parameters including origin date and demographic growth patterns of Indian subtype C were estimated using a Bayesian coalescent-based approach under relaxed molecular clock models.

Findings

The majority of the analyzed Indian and South African HIV-1 subtype C sequences formed a single monophyletic cluster. The most recent common ancestor date was calculated to be 1975.56 (95% HPD, 1968.78–1981.52). Reconstruction of the effective population size revealed three phases of epidemic growth: an initial slow growth, followed by exponential growth, and then a plateau phase approaching present time. Stabilization of the epidemic growth phase correlated with the foundation of National AIDS Control Organization in India.

Interpretation

Indian subtype C originated from a single South African lineage in the middle of 1970s. The current study emphasizes not only the utility of HIV-1 sequence data for epidemiological studies but more notably highlights the effectiveness of community or government intervention strategies in controlling the trend of the epidemic.     

Molecular Evolution of the HIV-1 Thai Epidemic between the Time of RV144 Immunogen Selection to the Execution of the Vaccine Efficacy Trial

The RV144 HIV-1 vaccine trial (Thailand, 2003 to 2009), using immunogens genetically matched to the regional epidemic, demonstrated the first evidence of efficacy for an HIV-1 vaccine. Here we studied the molecular evolution of the HIV-1 epidemic from the time of immunogen selection to the execution of the efficacy trial. We studied HIV-1 genetic diversity among 390 volunteers who were deferred from enrollment in RV144 due to preexisting HIV-1 infection using a multiregion hybridization assay, full-genome sequencing, and phylogenetic analyses. The subtype distribution was 91.7% CRF01_AE, 3.5% subtype B, 4.3% B/CRF01_AE recombinants, and 0.5% dual infections. CRF01_AE strains were 31% more diverse than the ones from the 1990s Thai epidemic. Sixty-nine percent of subtype B strains clustered with the cosmopolitan Western B strains. Ninety-three percent of B/CRF01_AE recombinants were unique; recombination breakpoint analysis showed that these strains were highly embedded within the larger network that integrates recombinants from East/Southeast Asia. Compared to Thai sequences from the early 1990s, the distance to the RV144 immunogens increased 52% to 68% for CRF01_AE Env immunogens and 12% to 29% for subtype B immunogens. Forty-three percent to 48% of CRF01_AE sequences differed from the sequence of the vaccine insert in Env variable region 2 positions 169 and 181, which were implicated in vaccine sieve effects in RV144. In conclusion, compared to the molecular picture at the early stages of vaccine development, our results show an overall increase in the genetic complexity of viruses in the Thai epidemic and in the distance to vaccine immunogens, which should be considered at the time of the analysis of the trial results.     

Evolution of the human immunodeficiency virus type 1 subtype-specific V3 domain is confined to a sequence space with a fixed distance to the subtype consensus.

Human immunodeficiency virus type 1 (HIV-1) strains can be separated into genetic subtypes based on phylogenetic analysis of the envelope gene. Once it had been shown that population-wide intrasubtype genetic variation of HIV-1 strains increases in the course of the AIDS epidemic, it remained uncertain whether HIV-1 subtypes are phenotypic entities spreading as distinct virus populations. To examine this, we applied Eigen's concepts of sequence geometry and fitness topography to the analysis of intrasubtype evolution of the gp120 V3 domain of HIV-1 subtypes A, B, C, and D in the course of the global AIDS epidemic. We observed that despite the high evolution rate of HIV-1, the nonsynonymous distances to the subtype consensus of sequences obtained early in the epidemic are similar to those obtained more than 10 years later, in contrast to the synonymous distances, which increased steadily over time. For HIV-1 subtype B, we observed that the evolution rate of the individual sequences is independent of their distance from the subtype B consensus, but for the individual sequences most distant from the consensus evolution away from the consensus is constrained. As a result, individual HIV-1 genomes fluctuate within a sequence space with fixed distance to the subtype consensus. Our findings suggest that the evolution of the V3 domain of HIV-1 subtypes A, B, C, and D is confined to an area in sequence space within a fixed distance to the consensus of a respective subtype. This in turn indicates that each HIV-1 subtype is a distinct viral quasispecies that is well adapted to the present environment, able to maintain its identity in the V3 region over time, and unlikely to merge during progression of the AIDS epidemic.     

Dispersion of the HIV-1 Epidemic in Men Who Have Sex with Men in the Netherlands: A Combined Mathematical Model and Phylogenetic Analysis

Background

The HIV-1 subtype B epidemic amongst men who have sex with men (MSM) is resurgent in many countries despite the widespread use of effective combination antiretroviral therapy (cART). In this combined mathematical and phylogenetic study of observational data, we aimed to find out the extent to which the resurgent epidemic is the result of newly introduced strains or of growth of already circulating strains.

Methods and Findings

As of November 2011, the ATHENA observational HIV cohort of all patients in care in the Netherlands since 1996 included HIV-1 subtype B polymerase sequences from 5,852 patients. Patients who were diagnosed between 1981 and 1995 were included in the cohort if they were still alive in 1996. The ten most similar sequences to each ATHENA sequence were selected from the Los Alamos HIV Sequence Database, and a phylogenetic tree was created of a total of 8,320 sequences. Large transmission clusters that included ≥10 ATHENA sequences were selected, with a local support value ≥ 0.9 and median pairwise patristic distance below the fifth percentile of distances in the whole tree. Time-varying reproduction numbers of the large MSM-majority clusters were estimated through mathematical modeling. We identified 106 large transmission clusters, including 3,061 (52%) ATHENA and 652 Los Alamos sequences. Half of the HIV sequences from MSM registered in the cohort in the Netherlands (2,128 of 4,288) were included in 91 large MSM-majority clusters. Strikingly, at least 54 (59%) of these 91 MSM-majority clusters were already circulating before 1996, when cART was introduced, and have persisted to the present. Overall, 1,226 (35%) of the 3,460 diagnoses among MSM since 1996 were found in these 54 long-standing clusters. The reproduction numbers of all large MSM-majority clusters were around the epidemic threshold value of one over the whole study period. A tendency towards higher numbers was visible in recent years, especially in the more recently introduced clusters. The mean age of MSM at diagnosis increased by 0.45 years/year within clusters, but new clusters appeared with lower mean age. Major strengths of this study are the high proportion of HIV-positive MSM with a sequence in this study and the combined application of phylogenetic and modeling approaches. Main limitations are the assumption that the sampled population is representative of the overall HIV-positive population and the assumption that the diagnosis interval distribution is similar between clusters.

Conclusions

The resurgent HIV epidemic amongst MSM in the Netherlands is driven by several large, persistent, self-sustaining, and, in many cases, growing sub-epidemics shifting towards new generations of MSM. Many of the sub-epidemics have been present since the early epidemic, to which new sub-epidemics are being added.     

广西壮族自治区HIV-1流行毒株的基因序列测定和亚型分析

使用ＰＣＲ技术对１４份广西ＨＩＶ－１阳性感染者外周血单核细胞（ＰＢＭＣｓ）样品进行扩增,获得ＨＩＶ－１膜蛋白（ｅｎｖ）基因的核酸片段,并对其Ｃ２－Ｖ３及邻区３５０－４５０个核苷酸序列进行了测定和分析。结果表明,１４份样品中９份为泰国Ｂ（Ｂ′）亚型,５份为Ｅ亚型毒株。其中Ｂ′亚型毒株的基因离散率为４．２％,与Ａ－Ｅ参考亚型及部分Ｂ亚型代表株序列相比较,与包括泰国、缅甸及云南德宏在内的Ｂ亚型毒株序列十分接近,相互之间基因离散率在３．０％－４．４％的范围内;而Ｅ亚型毒株的基因离散率为２．１％,与国际Ｅ亚型毒株的基因离散率最近,为５．６％,与其它国际参考亚型基因离散率很远,在２１．１％－２７．３％。根据以上数据及其它资料提示,广西存在Ｂ′和Ｅ两种亚型的ＨＩＶ－１的流行,且其Ｂ′亚型毒株的传入,与流行在云南德宏州的相同亚型ＨＩＶ－１毒株密切相关,而Ｅ亚型毒株则可能是由泰国经越南传入广西的     

重组CHO细胞C_(28)株S基因序列的测定及分析

目的测定重组CHO细胞C28株S基因序列,研究其遗传稳定性,并与已全基因序列测定的乙型肝炎病毒的S基因序列进行比较分析,预测和揭示现有疫苗株对当前疾病流行株的防病效果。方法从C28株中选取第22代、24代2、5代2、7代、28代2、9代3、0代、31代3、2代3、3代和34代细胞,根据GenBank中C基因型adr亚型乙型肝炎病毒的全基因序列设计引物。采用酚-氯仿法抽提CHO细胞基因组DNA,用PCR法扩增各代次细胞的S基因,回收700 bp左右的目的片段,克隆至pMD18-T载体上进行序列测定。利用生物学软件MEGA4.1和BioEdit进行S基因序列同源性分析,绘制系统进化树,分析与其他HBV病毒株S基因的同源性。应用实验动物测定C28株生产的重组乙型肝炎疫苗的效价。结果 C28株十一个代次之间S基因序列核苷酸和氨基酸同源性均为100%;C28株十一个代次S基因与其他病毒株S基因比较,与C基因型乙型肝炎病毒同源性最高,与其他基因型乙型肝炎病毒的核苷酸同源性达91.4%～95.1%,氨基酸同源性达84.5%～93.3%。免疫NIH小鼠结果显示5批重组乙型肝炎疫苗的效价均符合标准。结论 C28株S基因在传代及保存过程中具有较高的稳定性,对当前疾病流行株有较好的防病效果。     

High-resolution molecular epidemiology and evolutionary history of HIV-1 subtypes in Albania

Background

HIV-1 epidemic in Western Europe is largely due to subtype B. Little is known about the HIV-1 in Eastern Europe, but a few studies have shown that non-B subtypes are quite common. In Albania, where a recent study estimated a ten-fold increase of AIDS incidence during the last six years, subtype A and B account for 90% of the know infections.

Methodology/Principal Findings

We investigated the demographic history of HIV-1 subtype A and B in Albania by using a statistical framework based on coalescent theory and phylogeography. High-resolution phylogenetic and molecular clock analysis showed a limited introduction to the Balkan country of subtype A during the late 1980s followed by an epidemic outburst in the early 1990s. In contrast, subtype B was apparently introduced multiple times between the mid-1970s and mid-1980s. Both subtypes are growing exponentially, although the HIV-1A epidemic displays a faster growth rate, and a significantly higher basic reproductive number R₀. HIV-1A gene flow occurs primarily from the capital Tirane, in the center of the country, to the periphery, while HIV-1B flow is characterized by a balanced exchange between center and periphery. Finally, we calculated that the actual number of infections in Albania is at least two orders of magnitude higher than previously thought.

Conclusions/Significance

Our analysis demonstrates the power of recently developed computational tools to investigate molecular epidemiology of pathogens, and emphasize the complex factors involved in the establishment of HIV-1 epidemics. We suggest that a significant correlation exists between HIV-1 exponential spread and the socio-political changes occurred during the Balkan wars. The fast growth of a relatively new non-B epidemic in the Balkans may have significant consequences for the evolution of HIV-1 epidemiology in neighboring countries in Eastern and Western Europe.     

Phylogenetic analyses of Texas isolates indicate an evolving subtype of the clade B feline immunodeficiency viruses

Rigorous phylogenetic analyses were used to compare the nucleotide sequences of feline immunodeficiency virus strains isolated from Texas and throughout the world. The envelope V3-V4 sequences and capsid gene of the Texas isolates formed a cluster between subtypes B and E. Statistical comparisons with other published sequences confirmed that the Texas group is a unique cluster, possibly a new subtype, arising from subtype B.     

HIV infection in India: Epidemiology, molecular epidemiology and pathogenesis

The year 1986 saw first case of HIV infection as well as first report of AIDS case in India. Since then the epidemic has spread throughout the country. In the recent years there is evidence of epidemic being stabilized with decrease in new infections reported from some parts of the country. The absolute number of HIV infections in the country is expected to be close to 2.5 million and National AIDS Control Programme, phase III is geared to contain the epidemic. HIV viruses circulating in India predominantly belong to HIV-1 subtype C. However, there have been occasional reports of HIV-1 subtype A and B. Matter of concern is reports of A/C and B/C mosaic viruses that are being reported from different parts of the country. The data on HIV drug resistance from India is rather limited. Most of the studies have shown that the virus strains from drug naïve patients do not show significant level of drug resistance mutations. The few immunological studies in Indian patients show that the Indian HIV infected patients show both HIV-specific CTL responses as well as neutralizing antibody response. Mapping of CTL epitopes showed that while Indian patients identify same regions of Gag antigen as recognized by South African subtype C infected patients, some regions are uniquely recognized by Indian patients. There are very few studies on host genetic factors in India in context with HIV infection. However there are evidences reported of association of host genetic factors such as HLA types and haplotypes and HIV disease.     

HIV-1 subtype B epidemic and transmission patterns in Slovenia

In the present study the epidemic of human immunodeficiency virus type 1 (HIV-1) subtype B in Slovenia during the 10-year period was investigated using phylogenetic analysis of pol gene sequences. 119 pol sequences generated on samples dated from January 1996 to December 2005 were retrieved from the database of Slovenian HIV/AIDS Reference Laboratory. The phylogenetic analysis revealed 14 potentially significant transmission clusters (bootstrap value > or = 98%), comprising 34 HIV-1 strains. The vast majority of clustered individuals were men (91%), and of them, 79% were men who have sex with men. Factors significantly associated with clustering were: recent infection (HIV-1 infection during or after year 2003), diagnosis of primary HIV-1 infection, higher CD4 cell count and acquiring HIV-1 infection in Slovenia. Recent subtype B HIV-1 infections are the important driving force of current HIV-1 epidemic in Slovenia.     

Recent Evolutionary History of Human Immunodeficiency Virus Type 1 Subtype B: Reconstruction of Epidemic Onset Based on Sequence Distances to the Common Ancestor

We obtained and studied HIV-1 sequences with a known sampling year from three outbreaks of the HIV-1 epidemic: 141 env V3 (270 nt) sampled between 1984 and 1992 and 117 pol prot/RT (804 nt) sequences sampled between 1986 and 1999 from Dutch homosexual men and injecting drug users (IDUs), as well as 77 env V3 sequences sampled between 1983 and 1994 in the United States. Since retrospective serological and/or epidemiological data on these populations are available, providing estimates of the dates of the onset of the HIV-1 epidemics, we had the opportunity to test different phylogenetic models for their accuracy in deriving the recent evolutionary history of HIV-1 subtype B and the onset date of the HIV-1 epidemic. We observed that, in any given year, individual sequences vary widely in their distances to the common ancestor, and sequences close to the ancestors were found decades after the onset of the epidemic. Nevertheless, the mean evolutionary distances of virus strains to ancestors were increasing significantly during the course of the studied epidemics, which indicates that the molecular clock is operational in the recent evolution of HIV-1. When the relationship between the sampling years of sequences and their nucleotide distances to the common ancestor was extrapolated to the past, analysis of pol sequences provided accurate estimates of the onset years of the epidemics, whereas analysis of V3 sequences by the maximum-likelihood or neighbor-joining methods led to an overestimation of the age of the epidemics. Separate analysis of nonsynonymous and synonymous distances revealed that this overestimation results from nonsynonymous substitutions, whose numbers were not increasing significantly in all three virus populations over the observation period. In contrast, analysis of synonymous env V3 distances provided accurate estimates of the onset years for the outbreaks we studied. Received: 26 October 2001 / Accepted: 8 November 2001     

Concurrent evolution of human immunodeficiency virus type 1 in patients infected from the same source: rate of sequence change and low frequency of inactivating mutations.

Direct sequencing of segments of the envelope gene of human immunodeficiency virus type 1 proviruses in peripheral blood mononuclear cells has revealed that a cohort of hemophiliacs who were infected after exposure to a single common batch of factor VIII share closely related virus strains. Seventy-four sequences extending from hypervariable regions V4 through V5 from nine patients yielded a mean intrapatient nucleotide distance of 5.5%, while a mean of 4.2% was observed in 39 sequences of the V3 loop (six patients). Phylogenetic analysis revealed that sequences of six Edinburgh patients were particularly closely related and those from a patient infected in the United States were very distinct. The mean nucleotide distance among these six was 8.3%, while the mean distance from the U.S.-derived sequences was 25.5% in the V4-V5 region. The rate of sequence change across this patient group has been estimated to be 0.4% per year in the V4-V5 region and 0.5% per year in the V3 region, with at least a twofold range across patients. Only two inactivating nucleotide substitutions have been observed in a total of 42 kb of sequence obtained from the env and gag genes during this study.     

Identification of Specific Gene Sequences Conserved in Contemporary Epidemic Strains of Salmonella enterica

Genetic elements specific to recent and contemporary epidemic strains of Salmonella enterica were identified using comparative genomic analysis. Two epidemic multidrug-resistant (MDR) strains, MDR Salmonella enterica serovar Typhimurium definitive phage type 104 (DT104) and cephalosporin-resistant MDR Salmonella enterica serovar Newport, and an epidemic pansusceptible strain, Salmonella serovar Typhimurium DT160, were subjected to Salmonella gene microarray and suppression subtractive hybridization analyses. Their genome contents were compared with those of coexisting sporadic strains matched by serotype, geographic and temporal distribution, and host species origin. These paired comparisons revealed that epidemic strains of S. enterica had specific genes and gene regions that were shared by isolates of the same subtype. Most of these gene sequences are related to mobile genetic elements, including phages, plasmids, and plasmid-like and transposable elements, and some genes may encode proteins conferring growth or survival advantages. The emergence of epidemic MDR strains may therefore be associated with the presence of fitness-associated genetic factors in addition to their antimicrobial resistance genes.     

Genotyping of Tunisian hepatitis B virus isolates based on the sequencing of preS2 and S regions

The S nucleotide sequences of five hepatitis B virus strains isolated from plasma samples of Tunisian patients with chronic hepatitis B were determined; the preS2 region of three of them were sequenced. According to the comparative analysis of S peptide sequences with the reported sequences in the database bank, the five hepatitis B strains were shown to be related to the D genotypic group, subtype ayw. The nature of residues at positions 125 and 127 allowed us to distinguish between each subtype of the D group and to class all five Tunisian sequences in the 'ayw2' subtype. Moreover, two of them (1366 and 523) contained a substitution of the invariant Cys69 by Arg and Cys221 by Phe, respectively. Potential structural modifications due to the Cys-Arg change are discussed.     

HIV—1抗体阳性血浆中HIV—1病毒基因分型研究

为了解ＨＩＶ抗体阳性血浆中的ＨＩＶ１病毒基因亚型的情况,应用逆转录ＰＣＲ和ＤＮＡ序列测定技术,对６份获自高危人群的抗ＨＩＶ１阳性血浆进行序列分析和基因亚型分型的研究,结果表明均属ＨＩＶ１Ｂ亚型。Ｖ３环氨基酸序列分析指出这些ＨＩＶ１Ｂ亚型病毒株与泰国ＨＩＶ１Ｂ亚型病毒株核苷酸和氨基酸序列相似;同时发现ＨＩＶ１ｃＤＮＡ和氨基酸序列均相同,推测这６份标本可能来自同时感染同一株ＨＩＶ病毒的感染者。本研究对了解高危人群中ＨＩＶ１流行的遗传变异和ＨＩＶ１亚型病毒株的分子流行病分析具有一定的意义。